protected override void Context()
{
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_geneExpressionsDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
_applicationController = A.Fake <IApplicationController>();
sut = new EditMoleculeTask <Individual>(_moleculeExpressionTask, _applicationController);
_expressionProfileSelectionPresenter = A.Fake <IExpressionProfileSelectionPresenter>();
A.CallTo(() => _applicationController.Start <IExpressionProfileSelectionPresenter>()).Returns(_expressionProfileSelectionPresenter);
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_individual = new Individual {
OriginData = new OriginData {
Species = new Species {
Name = "Human", DisplayName = "Human"
}
}
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
}
protected override void Context()
{
_individual = new Individual();
_individual.OriginData = new OriginData();
_individual.OriginData.Species = new Species().WithName("Human");
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_executionContext = A.Fake <IExecutionContext>();
_proteinExpressionPresenter = A.Fake <IProteinExpressionsPresenter>();
_simpleMoleculePresenter = A.Fake <ISimpleMoleculePresenter>();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_applicationController = A.Fake <IApplicationController>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_containerTask = A.Fake <IContainerTask>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_proteinExpressionDbPathManager = A.Fake <IProteinExpressionsDatabasePathManager>();
A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter);
A.CallTo(() => _applicationController.Start <ISimpleMoleculePresenter>()).Returns(_simpleMoleculePresenter);
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
A.CallTo(() => proteinFactory.CreateFor(_individual)).Returns(_molecule);
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameter.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameter.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameter.HALF_LIFE_INTESTINE));
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
sut = new MoleculeExpressionTask <Individual>(_applicationController, _executionContext,
_individualMoleculeFactoryResolver, _querySettingsMapper,
_containerTask, _proteinExpressionDbPathManager,
_ontogenyRepository, _transportContainerUpdater, _moleculeParameterRepository, _subjectExpressionTask, _ontogenyTask);
}
protected override void Context()
{
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.AddMoleculeTo(_individual, A <string> ._)).Returns(_molecule);
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
sut = new MoleculeExpressionTask <Individual>(
_executionContext,
_individualMoleculeFactoryResolver,
_subjectExpressionTask,
_expressionProfileUpdater
);
}
protected override void Context()
{
base.Context();
_allParameters.Clear();
_allParameters.Add(_para1);
_individual = new Individual().WithName("toto");
_individualMolecule = new IndividualEnzyme();
_para1.Name = CoreConstants.Parameters.REFERENCE_CONCENTRATION;
_individualMolecule.Add(_para1);
_individualMolecule.Name = "CYP3A4";
_individual.AddMolecule(_individualMolecule);
}
private void updateOntogeny(IndividualMolecule molecule)
{
var liver = molecule.ExpressionContainer(CoreConstants.Organ.Liver);
if (liver == null)
{
return;
}
var ontogenyFactorLiver = liver.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
if (ontogenyFactorLiver != null)
{
molecule.Add(ontogenyFactorLiver);
}
IParameter ontogenyFactorDuodenum = null;
var duodenum = molecule.ExpressionContainer(CoreConstants.Compartment.Duodenum);
if (duodenum != null)
{
ontogenyFactorDuodenum = duodenum.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
}
//remove old ontogeny factor parameter in container
foreach (var expressionContainer in molecule.AllExpressionsContainers())
{
var ontogenyFactor = expressionContainer.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
if (ontogenyFactor != null)
{
expressionContainer.RemoveChild(ontogenyFactor);
}
}
if (ontogenyFactorDuodenum != null)
{
ontogenyFactorDuodenum.Name = CoreConstants.Parameters.ONTOGENY_FACTOR_GI;
molecule.Add(ontogenyFactorDuodenum);
}
}
private void updateLiverMoleculeExpression(IndividualMolecule molecule)
{
var liverContainer = molecule.ExpressionContainer(CoreConstants.Organ.Liver);
if (liverContainer == null)
{
return;
}
LIVER_ZONES.Each(z =>
{
var zoneContainer = _cloner.Clone(liverContainer).WithName(z);
zoneContainer.OrganPath.Add(z);
zoneContainer.ContainerName = z;
molecule.Add(zoneContainer);
});
molecule.RemoveChild(liverContainer);
}
protected override void Context()
{
base.Context();
_moleculeParameterAsAdvanced = A.Fake <IParameter>();
_molecule = new IndividualEnzyme();
_population = new RandomPopulation {
Settings = new RandomPopulationSettings {
BaseIndividual = new Individual()
}
};
_population.Add(new AdvancedParameterCollection());
_population.AddMolecule(_molecule);
A.CallTo(() => _entityPathResolver.PathFor(_moleculeParameterAsAdvanced)).Returns("A|B");
_molecule.Add(_moleculeParameterAsAdvanced);
_advancedParameter = new AdvancedParameter {
ParameterPath = "A|B", Name = "A|B"
};
_population.AddAdvancedParameter(_advancedParameter);
_population.AddAdvancedParameter(new AdvancedParameter {
ParameterPath = "ANOTHER PARAMETER", Name = "ANOTHER PARAMETER"
});
}
protected override void Context()
{
base.Context();
_enzymeExpression1 = new IndividualEnzyme().WithName("meta1");
_enzymeExpression2 = new IndividualEnzyme().WithName("meta2");
_enzymeExpressionClone1 = new IndividualEnzyme().WithName("meta1");
//Create a parameter that changed!
_userDefinedParameter = DomainHelperForSpecs.ConstantParameterWithValue(10);
_userDefinedParameter.DefaultValue = _defaultValue;
_enzymeExpressionClone1.Add(_userDefinedParameter);
_enzymeExpressionClone2 = new IndividualEnzyme().WithName("meta2");
_enzymeExpressionClone1.Ontogeny = new DatabaseOntogeny();
_enzymeExpressionClone2.Ontogeny = new DatabaseOntogeny();
_allEnzymesExpression = new List <IndividualMolecule> {
_enzymeExpression1, _enzymeExpression2
};
A.CallTo(() => _sourceIndividual.AllMolecules()).Returns(_allEnzymesExpression);
A.CallTo(() => _cloner.Clone(_enzymeExpression1)).Returns(_enzymeExpressionClone1);
A.CallTo(() => _cloner.Clone(_enzymeExpression2)).Returns(_enzymeExpressionClone2);
}
private void addHalfLifeToMolecule(IndividualMolecule individualMolecule)
{
individualMolecule.Add(_cloner.Clone(_defaultMolecule.HalfLifeLiver));
individualMolecule.Add(_cloner.Clone(_defaultMolecule.HalfLifeIntestine));
}
